Pallen, Mark J.


Publications (4)

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database

Citation
Pallen et al. (2022). International Journal of Systematic and Evolutionary Microbiology 72 (9)
Names (7)
“Paenistieleria cafavia” “Afabiota” “Afabiia” “Afabiales” “Afabiaceae” “Afabia” “Afabia udivosa”
Subjects
Ecology, Evolution, Behavior and Systematics General Medicine Microbiology Modeling and Simulation
Abstract
Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis

Citation
Pallen (2021). International Journal of Systematic and Evolutionary Microbiology 71 (9)
Subjects
Ecology, Evolution, Behavior and Systematics General Medicine Microbiology
Abstract
The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Citation
Gilroy et al. (2021). PeerJ 9
Names (94)
“Mediterraneibacter excrementigallinarum” “Ruthenibacterium merdavium” “Gemmiger stercoravium” “Eisenbergiella intestinipullorum” “Merdibacter merdavium” “Enterocloster excrementipullorum” “Borkfalkia stercoripullorum” “Gemmiger stercoripullorum” “Merdibacter merdigallinarum” “Intestinimonas stercoravium” “Limosilactobacillus intestinipullorum” “Mediterraneibacter pullistercoris” “Faecalibacterium gallistercoris” “Borkfalkia excrementigallinarum” “Mediterraneibacter stercoripullorum” “Anaerotignum merdipullorum” “Fusicatenibacter merdavium” “Anaerostipes excrementavium” “Blautia pullistercoris” “Hungatella pullicola” “Borkfalkia faecipullorum” “Acetatifactor stercoripullorum” “Mediterraneibacter vanvlietii” “Eisenbergiella stercoravium” “Butyricicoccus avistercoris” “Blautia stercorigallinarum” “Acutalibacter stercorigallinarum” “Mediterraneibacter excrementavium” “Corynebacterium faecigallinarum” “Phocaeicola excrementigallinarum” “Blautia merdavium” “Anaerostipes avistercoris” “Dietzia intestinigallinarum” “Mediterraneibacter faecigallinarum” “Mediterraneibacter faecipullorum” “Dietzia intestinipullorum” “Alistipes stercoravium” “Eisenbergiella merdavium” “Ligilactobacillus avistercoris” “Eisenbergiella merdigallinarum” “Nosocomiicoccus stercorigallinarum” “Mailhella merdavium” “Fournierella excrementigallinarum” “Fournierella merdavium” “Desulfovibrio gallistercoris” “Blautia merdipullorum” “Phocaeicola faecigallinarum” “Alistipes avicola” “Bariatricus faecipullorum” “Desulfovibrio intestinavium” “Brachybacterium merdavium” “Brevibacterium intestinavium” “Agathobaculum intestinipullorum” “Limosilactobacillus excrementigallinarum” “Mediterraneibacter merdigallinarum” “Fournierella merdigallinarum” “Mediterraneibacter pullicola” “Mediterraneibacter merdipullorum” “Microbacterium stercoravium” “Collinsella stercoripullorum” “Ligilactobacillus excrementavium” “Mucispirillum faecigallinarum” “Janibacter merdipullorum” “Lactobacillus pullistercoris” “Atopostipes pullistercoris” “Gemmiger excrementavium” “Fournierella merdipullorum” “Ruania gallistercoris” “Tidjanibacter faecipullorum” “Companilactobacillus pullicola” “Rothia avicola” “Rubneribacter avistercoris” “Sphingobacterium stercorigallinarum” “Intestinimonas merdavium” “Luteimonas excrementigallinarum” “Alistipes intestinigallinarum” “Tetragenococcus pullicola” “Eisenbergiella pullistercoris” “Agathobaculum merdavium” “Evtepia faecavium” “Barnesiella excrementavium” “Acutalibacter pullistercoris” “Anaerofilum excrementigallinarum” “Evtepia faecigallinarum” “Gemmiger excrementipullorum” “Anaerobiospirillum pullistercoris” “Acinetobacter avistercoris” “Limosilactobacillus merdigallinarum” “Desulfovibrio intestinigallinarum” “Blautia stercoravium” “Barnesiella excrementigallinarum” “Gemmiger faecavium” “Alectryobacillus” “Alectryobacillus merdavium”
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.